C taxonomy (#20)

* taxonomy getParents and getParentsMany

* 1.6.0

package.json

@@ -1,6 +1,6 @@
 {
   "name": "node-mist3",
-  "version": "1.5.5",
+  "version": "1.6.0",
   "description": "Helper package to deal with MiST3 API",
   "main": "src/index.js",
   "scripts": {

src/Taxonomy.js

@@ -0,0 +1,95 @@
+'use strict'
+
+const https = require('https')
+const bunyan = require('bunyan')
+
+const NodeMist3 = require('./NodeMist3Abstract')
+
+const kDefaults = {
+	maxRequests: 30
+}
+
+module.exports =
+class Taxonomy extends NodeMist3 {
+	constructor(options, logLevel = 'info') {
+		super(options)
+		this.log = bunyan.createLogger(
+			{
+				name: 'node-mist3-taxonomy',
+				level: logLevel
+			}
+		)
+	}
+
+	getParents(taxid, options = {skipFailed: false}) {
+		this.log.info(`Getting parents of taxid: ${taxid} with options ${JSON.stringify(options)}`)
+		this.httpsOptions.method = 'GET'
+		this.httpsOptions.path = `/v1/taxonomy/${taxid}/parents`
+		return new Promise((resolve, reject) => {
+			const request = https.request(this.httpsOptions, (response) => {
+				if (response.statusCode === 504) {
+					if (options.skipFailed){
+						this.log.warn(`taxid ${taxid} ::: ${response.statusCode} - ${response.statusMessage}`)
+						return resolve([])
+					}
+					else {
+						this.log.error(`taxid ${taxid} ::: ${response.statusCode} - ${response.statusMessage}`)
+						return reject(response.statusCode)
+					}
+				}
+				const chunks = []
+				response.on('data', (chunk) => chunks.push(chunk))
+				response.on('end', () => {
+					const buffer = Buffer.concat(chunks)
+					let taxonomy = []
+					try {
+						taxonomy = JSON.parse(buffer)
+						resolve(taxonomy)
+					}
+					catch (err) {
+						if (options.skipFailed === true){
+							this.log.warn(buffer.toString())
+							resolve([])
+						}
+						else {
+							console.log('hey')
+							this.log.error(buffer.toString())
+							reject(err)
+						}
+					}
+				})
+				response.on('error', (err) => {
+					this.log.fatal(err)
+					reject(err)
+				})
+			})
+			request.end()
+		})
+	}
+
+	getParentsMany(taxids, options = {skipFailed: true}) {
+		const tmpTaxids = []
+		taxids.forEach((taxid) => tmpTaxids.push(taxid))
+		this.log.info(`getting taxonomy from ${tmpTaxids.length} taxids`)
+		const self = this
+		async function asyncGetMany (listOfTaxids) {
+			const allResponses = []
+			self.log.debug(`Full list: ${listOfTaxids}`)
+			while (listOfTaxids.length !== 0) {
+				const requests = []
+				const batch = listOfTaxids.splice(0, kDefaults.maxRequests)
+				self.log.debug(`new Batch: ${batch}`)
+				batch.forEach((taxid) => requests.push(self.getParents(taxid, options)))
+				await Promise.all(requests).then((responses) => {
+					responses.forEach((response) => {
+						allResponses.push(response)
+					})
+				}).catch((err) => {
+					throw err
+				})
+			}
+			return allResponses
+		}
+		return asyncGetMany(tmpTaxids)
+	}
+}